Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_16G-N1-BDNA-1_B23KGCJLT4_1/1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/150d0b1beff4b4717c8d3d36e943a1/.command.sh
  Downloading: s3://ai-pipelines-experiment/chnobles/ref_data/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/150d0b1beff4b4717c8d3d36e943a1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_16G-N1-BDNA-1_B23KGCJLT4_1/1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_16G-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 92137048 total, 68059 skipped (flags/unmapped)
Fragments: 46171405 total (45845640 tlen-paired, 3896 hash-paired, 445 singletons, 20374 discordant, 301050 orphans, 13837 too large [>5000 bp], 18135166 duplicates)
Reads: 100242829 total, 55464 skipped (flags/unmapped)
Fragments: 50235195 total (49911582 tlen-paired, 2884 hash-paired, 600 singletons, 14758 discordant, 305371 orphans, 11473 too large [>5000 bp], 19353657 duplicates)
Reads: 99018773 total, 61253 skipped (flags/unmapped)
Fragments: 49625110 total (49258713 tlen-paired, 4391 hash-paired, 409 singletons, 18002 discordant, 343595 orphans, 25652 too large [>5000 bp], 19605413 duplicates)
Reads: 108517537 total, 90275 skipped (flags/unmapped)
Fragments: 54467512 total (53687526 tlen-paired, 3215 hash-paired, 469 singletons, 146181 discordant, 630121 orphans, 61414 too large [>5000 bp], 21579391 duplicates)